And on top of that there were located far away from the city which meant I would need to add an extra hour to my commute. 

The extra 40k is about $200 a month on a mortgage payment over a 30 year amortization period.Living in an apartment for $1000/month for 12 months= $12000I doubt they'll be a significant drop in a single year but let's say SFH go down 10%.

But at the end of 20 years I will be responsible for any extra payments if the interest rates are higher.

If the interest rate increase over the life of the loan and we don’t make any extra payments to the loan then we would have to pay a payment at the end of the 20 year loan.

With the current situation of adding bed and bath under ground, the appraisal appraised the proper at 134,000$... but there is a comp with the exact building, year, SqFt, and construction that sold January that year that has these extra bed and bath above ground and sold for 165,000$!

I would take the cash and go buy a small apartment complex that pays for my home, and give me extra cash flow as well.

I would assume my cpa would know about the extra taxes I would need to pay or would the Custodian of the Ira?

I paid around $150 to fix a broken lock, rekey multiple locks ,and provide extra new keys. 

If they have extra money, come find Rick. 

If there is a tool you both want, you can bid against each other above and beyond is assigned value paying the extra out of pocket with personal money.